PaperBLAST
PaperBLAST Hits for Pf1N1B4_4068 (85 a.a., MKSLTVGARA...)
Show query sequence
>Pf1N1B4_4068
MKSLTVGARAIELDKDGFLVELSDWSAEVAAALAAAEDIELSPEHWEILELLRSFYDEFQ
LSPATRPLIKYTALKLGPTRATACT
Running BLASTp...
Found 56 similar proteins in the literature:
PA2608 hypothetical protein from Pseudomonas aeruginosa PAO1
60% identity, 75% coverage
AL038_07465, BLE401_16850 TusE/DsrC/DsvC family sulfur relay protein from Beggiatoa leptomitoformis
41% identity, 74% coverage
- Comparative Genomics of Beggiatoa leptomitoformis Strains D-401 and D-402T with Contrasting Physiology but Extremely High Level of Genomic Identity
Rudenko, Microorganisms 2020 - “...AL038_07480 ALG67570.1 dsrE BLE401_16840 AUI70201.1 AL038_07475 ALG67569.1 dsrF BLE401_16845 AUI70202.1 AL038_07470 ALG67568.1 dsrH BLE401_16850 AUI70203.1 AL038_07465 ALG67567.1 dsrC BLE401_14535 AUI70655.1 AL038_09735 ALG69423.1 soeA BLE401_14540 AUI69788.1 AL038_09730 ALG67939.1 soeB BLE401_14545 AUI69789.1 AL038_09725 ALG67938.1 soeC...”
- “...BLE401_16835 AUI70200.1 AL038_07480 ALG67570.1 dsrE BLE401_16840 AUI70201.1 AL038_07475 ALG67569.1 dsrF BLE401_16845 AUI70202.1 AL038_07470 ALG67568.1 dsrH BLE401_16850 AUI70203.1 AL038_07465 ALG67567.1 dsrC BLE401_14535 AUI70655.1 AL038_09735 ALG69423.1 soeA BLE401_14540 AUI69788.1 AL038_09730 ALG67939.1 soeB BLE401_14545 AUI69789.1 AL038_09725 ALG67938.1 soeC...”
CBG46_00190 TusE/DsrC/DsvC family sulfur relay protein from Actinobacillus succinogenes
44% identity, 73% coverage
MHY1_00084 TusE/DsrC/DsvC family sulfur relay protein from Methylovirgula sp. HY1
38% identity, 73% coverage
- Sulfur and methane oxidation by a single microorganism
Gwak, Proceedings of the National Academy of Sciences of the United States of America 2022 - “...and MHY1_013611362; only MHY1_013611362 are indicated here), then transferred to the DsrEFH (MHY1_0008183) and DsrC (MHY1_00084) via the sulfur-transporting complex [rhodanese (MHY1_01281)-TusA (MHY1_00072)-DsrE2A (MHY1_00073)]. The persulfurated DsrC is oxidized to DsrC and sulfite by DsrAB sulfite reductase (MHY1_0007980), thereby releasing electrons to the ironsulfur flavoprotein, DsrL...”
- “...also found to contain sMMO and PMO gene clusters ( 26 ). The protein DsrC (MHY1_00084) is characterized by a conserved carboxyl-terminal motif (Cys B X 10 Cys A ) and plays a central role in the rDsr pathway, as it acts as a sulfur carrier...”
FOKN1_1950 TusE/DsrC/DsvC family sulfur relay protein from Thiohalobacter thiocyanaticus
37% identity, 74% coverage
LT988_06640 TusE/DsrC/DsvC family sulfur relay protein from Thiocapsa bogorovii
38% identity, 72% coverage
- The Complete Genome of a Novel Typical Species Thiocapsa bogorovii and Analysis of Its Central Metabolic Pathways
Petushkova, Microorganisms 2024 - “...the genome contains several more genes annotated as TusE/DsrC/DsvC family sulfur relay protein (LT988_03825, LT988_03875, LT988_06640, LT988_06690, LT988_16185, LT988_16425, and LT988_19515) according to GenBank. The results obtained were compared with the data on the possible pathways of sulfate oxidation in purple sulfur bacteria summarized in the...”
- “...LT988_06635 respiratory nitrate reductase subunit gamma 10 Alvin_1256 dsrC K23077 dissimilatory sulfite reductase related protein LT988_06640 TusE/DsrC/DsvC family sulfur relay protein 11 Alvin_1255 dsrH K07237 tRNA 2-thiouridine synthesizing protein B LT988_06645 tusB ; sulfurtransferase complex subunit TusB 12 Alvin_1254 dsrF K07236 tRNA 2-thiouridine synthesizing protein C...”
HD1815 putative sulfite reductase from Haemophilus ducreyi 35000HP
41% identity, 75% coverage
MOY_00165 TusE/DsrC/DsvC family sulfur relay protein from Halomonas sp. GFAJ-1
42% identity, 66% coverage
tusE / P0AB18 sulfur transfer protein TusE from Escherichia coli (strain K12) (see 2 papers)
TUSE_ECOLI / P0AB18 Sulfurtransferase TusE; tRNA 2-thiouridine synthesizing protein E; EC 2.8.1.- from Escherichia coli (strain K12) (see paper)
b0969 putative sulfite reductase (EC 1.8.-.-) from Escherichia coli str. K-12 substr. MG1655
S1037 sulfurtransferase TusE from Shigella flexneri 2a str. 2457T
EDL933_1237 sulfurtransferase TusE from Escherichia coli O157:H7 str. EDL933
44% identity, 73% coverage
- function: Part of a sulfur-relay system required for 2-thiolation of 5- methylaminomethyl-2-thiouridine (mnm(5)s(2)U) at tRNA wobble positions. Could accept sulfur from TusD.
subunit: Interacts with the TusBCD complex. Interacts with MnmA. - In Silico Prediction and Prioritization of Novel Selective Antimicrobial Drug Targets in Escherichia coli
Svanberg, Antibiotics (Basel, Switzerland) 2021 - “...trp operon leader peptide P0AD92 N/D N/D N/A 100% 100% 32 N/A tusE Sulfurtransferase TusE P0AB18 N/D Cytoplasm N/A 100% 90% 204 Essential wzyE Probable ECA polymerase P27835 N/D Cell inner membrane N/A 100% 87% 744 N/A ycaR UPF0434 protein YcaR P0AAZ7 N/D Cytoplasm N/A 100%...”
- EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference
Tian, Nucleic acids research 2004 - “...specific SIT evaluation' component of EFICAz. For example, b0969 is annotated in KEGG as a `putative, sulfite reductase [EC 1.8.99.3]'. Its closet homolog in...”
- “...with only one sequence. Since the sequence identity between b0969 and DSVC_DESVH is only 36% (below the 60% SIT), EFICAz cannot infer the function of b0969....”
- Addendum
, Open forum infectious diseases 2019 - The novel EHEC gene asa overlaps the TEGT transporter gene in antisense and is regulated by NaCl and growth phase
Vanderhaeghen, Scientific reports 2018 - “...of asa . Downstream of EDL933_1238 is a gene for tRNA 2-thiouridine synthesizing protein E (EDL933_1237), whichhas a trivial overlap witha gene for a putative acyl-phosphate phosphohydrolase (EDL933_1236) in antisense. Upstream of EDL933_1238 is a phage integrase (EDL933_1239, not shown) belonging to the O-island #44. Numbers...”
- “...overlapping antisense codon of asa . There is a tRNA 2-thiouridine synthesizing protein E gene (EDL933_1237) downstream of EDL933_1238, which trivially overlaps a putative acyl-phosphate phosphohydrolase gene (EDL933_1236) in antisense (Fig. 2 ). Upstream of the mother gene is the O-island #44 encoding the prophage CP-EDL933M....”
dsrC / O87899 DsrC monomer from Allochromatium vinosum (see 3 papers)
Alvin_1256 DsrC from Allochromatium vinosum DSM 180
D3RSN6 Sulfurtransferase from Allochromatium vinosum (strain ATCC 17899 / DSM 180 / NBRC 103801 / NCIMB 10441 / D)
36% identity, 72% coverage
- Evidence for autotrophic growth of purple sulfur bacteria using pyrite as electron and sulfur source
Alarcon, Applied and environmental microbiology 2024 - “...DsrK 2.168 2.94E-26 Alvin_1260 DsrJ 2.113 4.47E-15 Alvin_1261 DsrO 1.987 5.20E-20 Alvin_1262 DsrP 1.678 1.86E-15 Alvin_1256 DsrC 1.247 1.07E-07 sox genes Alvin_2111 SoxY 2.919 1.91E-41 Alvin_2112 SoxZ 2.40 2.39E-21 Alvin_2167 SoxB 1.22 2.19E-07 Alvin_2169 SoxA 1.175 0.00714587 Alvin_2168 SoxX 1.074 0.00178113 a Only those with a...”
- “...sulfur globules, genes related to Dsr are downregulated in the current study [except that dsrC (Alvin_1256) remained relatively unchanged in its expression level]. In fact, a review chapter on dissimilatory sulfur metabolism in purple sulfur bacteria pointed out that purple non-sulfur bacteria, including those able to...”
- The Complete Genome of a Novel Typical Species Thiocapsa bogorovii and Analysis of Its Central Metabolic Pathways
Petushkova, Microorganisms 2024 - “...DsrEFH (genes Alvin_1253, Alvin_1254, and Alvin_1255), which in its turn perform the persulfation of DsrC (Alvin_1256); persulfated DsrC is likely to serve as a direct substrate for reverse sulfite reductase DsrAB. Rhd_2599, TusA, and DsrE2 in Alc. vinosum DSM 180 T have been shown to bind...”
- “...dsrM K00374 nitrate reductase gamma subunit [EC:1.7.5.1 1.7.99.-] LT988_06635 respiratory nitrate reductase subunit gamma 10 Alvin_1256 dsrC K23077 dissimilatory sulfite reductase related protein LT988_06640 TusE/DsrC/DsvC family sulfur relay protein 11 Alvin_1255 dsrH K07237 tRNA 2-thiouridine synthesizing protein B LT988_06645 tusB ; sulfurtransferase complex subunit TusB 12...”
- A comparative quantitative proteomic study identifies new proteins relevant for sulfur oxidation in the purple sulfur bacterium Allochromatium vinosum
Weissgerber, Applied and environmental microbiology 2014 - “...Alvin_1251 Alvin_1252 Alvin_1253 Alvin_1254 Alvin_1255 Alvin_1256 Alvin_1257 Alvin_1258 Alvin_1259 Alvin_1260 Alvin_1261 Alvin_1262 Alvin_1263 Alvin_1264...”
- Genome-wide transcriptional profiling of the purple sulfur bacterium Allochromatium vinosum DSM 180T during growth on different reduced sulfur compounds
Weissgerber, Journal of bacteriology 2013 - “...Alvin_1251 Alvin_1252 Alvin_1253 Alvin_1254 Alvin_1255 Alvin_1256 Alvin_1257 Alvin_1258 Alvin_1259 Alvin_1260 Alvin_1261 Alvin_1262 Alvin_1263 Alvin_1264...”
- Complete Genome Sequence of Halomonas sp. Strain FeN2, a Novel Cathode-Oxidizing Bacterium Isolated from Catalina Harbor Sediments.
Vu, Microbiology resource announcements 2021 - “...sulfur metabolism genes found include fccA ( Q06529 ), soxX ( O66187 ), dsrC ( D3RSN6 ), soeB ( ADC63402.1 ), hdrB ( ADJ22501.1 ), and several sulfurtransferases, including tusB , tusC , and tusD . Our analysis of the FeN2 genome provides a valuable reference...”
- Diversity and Distribution of Sulfur Oxidation-Related Genes in Thioalkalivibrio, a Genus of Chemolithoautotrophic and Haloalkaliphilic Sulfur-Oxidizing Bacteria
Berben, Frontiers in microbiology 2019 - “...used for FccAB (Uniprot accessions: Q06529/Q06530), SoxAXYZB (Q1W3E4, D3RVS6, D3RVA1, D3RVA2, D3RVS5), DsrABC (O33998, D3RSN2, D3RSN6), AprBA (D3RSA0, D3RSA1), Sat (O66036) and SoeABC (NCBI accessions: ADC63403.1, ADC63402.1, ADC63401.1). For SQR a sequence from Acidithiobacillus ferrooxidans (B7JBP8) was used (a type I SQR), for SorAB sequences from...”
P45184 Sulfurtransferase TusE homolog from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
40% identity, 73% coverage
THER_0471 TusE/DsrC/DsvC family sulfur relay protein from Thermodesulfovibrio sp. N1
33% identity, 74% coverage
HAL1_10182 TusE/DsrC/DsvC family sulfur relay protein from Halomonas sp. HAL1
43% identity, 59% coverage
PMI0794 sulfite reductase from Proteus mirabilis HI4320
39% identity, 73% coverage
YE1597 putative sulfite reductase subunit protein from Yersinia enterocolitica subsp. enterocolitica 8081
42% identity, 70% coverage
LT988_16425 TusE/DsrC/DsvC family sulfur relay protein from Thiocapsa bogorovii
46% identity, 33% coverage
SVA_1949 TusE/DsrC/DsvC family sulfur relay protein from Sulfurifustis variabilis
39% identity, 67% coverage
- The complete genome sequences of sulfur-oxidizing Gammaproteobacteria Sulfurifustis variabilis skN76(T) and Sulfuricaulis limicola HA5(T)
Umezawa, Standards in genomic sciences 2016 - “...dsrAB (SVA_0258-0259, SCL_0256-0257), dsrS (SVA_2921, SCL_0781) and dsrC (SVA_0281, SVA_0284, SVA_0358, SVA_0917, SVA_0969, SVA_1205, SVA_1793, SVA_1949, SVA_2832, SVA_3655; SCL_0275, SCL_0524, SCL_0785, SCL_1279, SCL_1423, SCL_2646). As genes encoding proteins involved in oxidation of sulfite to sulfate in the cytoplasm, both genomes contain two copies of the aprAB...”
O28055 dissimilatory sulfite reductase (EC 1.8.99.5) from Archaeoglobus fulgidus (see paper)
AF_2228, WP_010879717 TusE/DsrC/DsvC family sulfur relay protein from Archaeoglobus fulgidus DSM 4304
AF2228 sulfite reductase, desulfoviridin-type subunit gamma (dsvC) from Archaeoglobus fulgidus DSM 4304
36% identity, 68% coverage
- A novel methoxydotrophic metabolism discovered in the hyperthermophilic archaeon Archaeoglobus fulgidus
Welte, Environmental microbiology 2021 - “...(AF_1340), sulfate adenylyltransferase Sat (AF_1667), adenylylsulfate reductase AprAB (AF_166970), dissimilatory sulfite reductase DsrAB (AF_04234), DsrC (AF_2228), quinonemodifying oxidoreductase QmoABC (AF_06613), molybdopterin oxidoreductase DsrMKJOP (AF_0499503), DsrMK(K) (AF_05435), F 420 H 2 :quinone oxidoreductase FqoJKMLNABCDHIF (AF_182333), soluble heterodisulfide reductase HdrABC (AF_13757), F 420 nonreducing hydrogenase VhuADG (AF_13724), F...”
- Determination of a novel structure by a combination of long-wavelength sulfur phasing and radiation-damage-induced phasing.
Weiss, Acta crystallographica. Section D, Biological crystallography 2004 (PubMed)- GeneRIF: The structure of the 115 amino-acid residue protein DsvC was determined based on the anomalous scattering provided by the five S atoms present in the structure
- The DsrD functional marker protein is an allosteric activator of the DsrAB dissimilatory sulfite reductase
Ferreira, Proceedings of the National Academy of Sciences of the United States of America 2022 - “...to gradual activity loss. Production of A. fulgidus DsrC. The A. fulgidus VC16 dsrC gene (AF2228) was amplified by PCR using genomic DNA and primers (#20/#21) with Nde I and Eco RI restriction sites, respectively. The amplified product was ligated into a pET-28a(+) vector (Novagen) resulting...”
- Identification of key components in the energy metabolism of the hyperthermophilic sulfate-reducing archaeon Archaeoglobus fulgidus by transcriptome analyses
Hocking, Frontiers in microbiology 2014 - “..., Figure S1A-I ). The notable exception was that of dsrD (AF0425) and dsrC transcripts (AF2228), which were expressed at lower levels (Table 1A , Figure S1A ) and were both induced in late-log S-L samples. These two genes had a corresponding transcriptional pattern (Pearson's r...”
- “...2005 ; Oliveira et al., 2008 ; Grein et al., 2010 ). The dsrC gene (AF2228) is, however, expressed at average transcriptional abundance vs. high transcriptional abundance for dsrAB (Table 1C , Figure S1 ). This is lower than previously estimated in D. vulgaris , where...”
VP1626 sulfite reductase, gamma subunit-related protein from Vibrio parahaemolyticus RIMD 2210633
35% identity, 73% coverage
- TssL2 of T6SS2 is required for mobility, biofilm formation, wrinkly phenotype formation, and virulence of Vibrio parahaemolyticus SH112
Bai, Applied microbiology and biotechnology 2024 - “...), and upregulated expression of biofilm-related genes ( cpsQ , aphA ), metabolism-related proteins (VP1647, VP1626, VPA0472), uncharacterized proteins (VP1279, VPA0668, VP1444, VPA1308), and which were consistent with the previous results (Wu et al. 2022 ). Therefore, another mechanism is that TssL2 deficiency changes smooth phenotype...”
Desca_2677 TusE/DsrC/DsvC family sulfur relay protein from Desulfotomaculum nigrificans CO-1-SRB
36% identity, 72% coverage
DESAMIL20_1431 TusE/DsrC/DsvC family sulfur relay protein from Desulfurella amilsii
34% identity, 65% coverage
- Insight into the sulfur metabolism of Desulfurella amilsii by differential proteomics
Florentino, Environmental microbiology 2019 - “...The alpha and beta subunits of the dissimilatory sulfite reductase (DsrAB, DESAMIL20_1434DESAMIL20_1435), together with DsrC (DESAMIL20_1431) and the DsrK subunit (DESAMIL20_1429) of the DsrMKJOP complex were also more abundant in thiosulfatereducing cultures. Only one peptide of the DsrM subunit (DESAMIL20_1430) of the DsrMK complex was identified...”
- “...with DsrAB/DsrC, and thus compensate for the absence of the second conserved Cys in DsrC (DESAMIL20_1431). In the acidothermophilic sulfuroxidizing archaeon Metallosphaera cuprina , two DsrE proteins were recently shown to be involved in thiosulfate transfer (Liu et al., 2014 ). Conspicuously, a third gene in...”
WP_202320007 TusE/DsrC/DsvC family sulfur relay protein from Archaeoglobus neptunius
36% identity, 68% coverage
SVA_1205 TusE/DsrC/DsvC family sulfur relay protein from Sulfurifustis variabilis
31% identity, 71% coverage
- The complete genome sequences of sulfur-oxidizing Gammaproteobacteria Sulfurifustis variabilis skN76(T) and Sulfuricaulis limicola HA5(T)
Umezawa, Standards in genomic sciences 2016 - “...gene cluster, dsrAB (SVA_0258-0259, SCL_0256-0257), dsrS (SVA_2921, SCL_0781) and dsrC (SVA_0281, SVA_0284, SVA_0358, SVA_0917, SVA_0969, SVA_1205, SVA_1793, SVA_1949, SVA_2832, SVA_3655; SCL_0275, SCL_0524, SCL_0785, SCL_1279, SCL_1423, SCL_2646). As genes encoding proteins involved in oxidation of sulfite to sulfate in the cytoplasm, both genomes contain two copies of...”
LT988_16185 TusE/DsrC/DsvC family sulfur relay protein from Thiocapsa bogorovii
31% identity, 69% coverage
MHY1_00075 TusE/DsrC/DsvC family sulfur relay protein from Methylovirgula sp. HY1
38% identity, 68% coverage
- Sulfur and methane oxidation by a single microorganism
Gwak, Proceedings of the National Academy of Sciences of the United States of America 2022 - “..., 71 , 72 ). Notably, two additional DsrC-like proteins are encoded in strain HY1 (MHY1_00075 and MHY1_00097). Both lack Cys A and probably function as regulatory sulfur-related proteins (RpsA) ( 73 ). In strain HY1, sulfite formed by the rDsr pathway does not appear to...”
LT988_06690 TusE/DsrC/DsvC family sulfur relay protein from Thiocapsa bogorovii
37% identity, 67% coverage
dsvC / P45573 DsvC monomer (D. vulgaris) from Desulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / NCIMB 8303 / VKM B-1760 / Hildenborough) (see 3 papers)
DSVC_NITV2 / P45573 Sulfite reductase, dissimilatory-type subunit gamma; Desulfoviridin subunit gamma; Hydrogensulfite reductase subunit gamma; EC 1.8.1.22 from Nitratidesulfovibrio vulgaris (strain ATCC 29579 / DSM 644 / CCUG 34227 / NCIMB 8303 / VKM B-1760 / Hildenborough) (Desulfovibrio vulgaris) (see 2 papers)
DVU2776, ORF03581 dissimilatory sulfite reductase, gamma subunit from Desulfovibrio vulgaris Hildenborough
34% identity, 72% coverage
- function: Catalyzes the reduction of sulfite to sulfide. This is the terminal oxidation reaction in sulfate respiration, a process catalyzed by the sulfate-reducing bacteria.
catalytic activity: [DsrC protein]-trisulfide + NAD(+) + 3 H2O = [DsrC protein]- dithiol + sulfite + NADH + 3 H(+) (RHEA:78943)
subunit: Heterohexamer of two alpha, two beta and two gamma subunits. - Origin of biogeographically distinct ecotypes during laboratory evolution
Valenzuela, Nature communications 2024 - “...updated the GPR of the reaction (rxn14403) as an OR relationship for the gene 208282 (DVU2776) because the sulfite reductase has been characterized to have multiple functions 72 , 73 . The published version of the iMR539 model consisted of 539 genes from Mm that were...”
- Synergistic epistasis enhances the co-operativity of mutualistic interspecies interactions
Turkarslan, The ISME journal 2021 - “...mutations in SR genes were among the top contributors to the total G-score in Dv (DVU2776 (74.7), DVU1295 (46.5), DVU0846 (42.9), and DVU0847 (22.3)). However, it was intriguing that DVU2776 (DsrC), which catalyzes the conversion of sulfite to sulfide, the final step in SR, accumulated function...”
- “...to uncover evidence for epistatic interactions in improving obligate syntrophy. Indeed, missense mutations in DsrC (DVU2776) were fixed simultaneously with the appearance of loss of function mutations in one of two sigma 54 type regulators (DVU2894, DVU2394) in lines HA2, and UR1 ( P =5.4010 5...”
- Proteomic and Isotopic Response of Desulfovibrio vulgaris to DsrC Perturbation
Leavitt, Frontiers in microbiology 2019 - “...the two strains. Proteins not found in this dataset are denoted with dashed boxes. DsrC (DVU2776) was substantially less expressed (1.13 0.22) in the mutant relative to the WT, as expected given the manipulation of dsrC expression in the mutant. From the membrane bound DsrMKJOP complex...”
- Towards a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough
Chhabra, PloS one 2011 - “...subunits (DsrA, DVU0402; DvsB (a.k.a. DsrB in D. vulgaris ), DVU0403; DsrD, DVU0404; and DsrC, DVU2776; respectively) [40] . Also known as desulfoviridin, the dissimilatory sulfite reductase complex from D. vulgaris has been reported to be an 2 2 2 structure [41] . The D. vulgaris...”
- “...99 DGYGPVGAWFLLFK * AK Methylation 2 99 DVU0846 (ApsB) SADSIMWTVK * FR Trimethylation 2 99 DVU2776 (DsrC) ESEGISDISPDHQK * IIDFLQDYYK Trimethylation / Acetylation 2 99 LK * EVYELFPSGPGK Trimethylation+Oxidation 1.7 98 DVU2927 (RplL) TGLGLK * EAK Methylation 2 99 ALTGLGLK * EAK Methylation 2 99 IGVIK...”
- Generalized schemes for high-throughput manipulation of the Desulfovibrio vulgaris genome
Chhabra, Applied and environmental microbiology 2011 - “...of three AGTtagged proteins from D. vulgaris, DsrC (DVU2776), MreB (DVU0789) (data not shown), and FtsZ (DVU2499), from the respective engineered strains to the...”
- Expression profiling of hypothetical genes in Desulfovibrio vulgaris leads to improved functional annotation
Elias, Nucleic acids research 2009 - “...other genes were expressed as well. The positive control was the constitutively expressed dsrC gene (DVU2776) with an average basal expression rate of 9.7, which would place it above the top 1/8th percentile cutoff of 11.8 so as to be placed in the highly expressed category....”
- “...Biosystems). To ensure the DNA was removed, PCR amplification of DVU0847 (adenylyl-sulphate reductase, -subunit) and DVU2776 (dissimilatory sulfite reductase, -subunit) was performed and yielded no PCR product (data not shown). cDNA was produced using the ImProm II Reverse Transcription System A3800 (Promega). PCR reactions were then...”
- Cell-wide responses to low-oxygen exposure in Desulfovibrio vulgaris Hildenborough
Mukhopadhyay, Journal of bacteriology 2007 - “...name dsrD apsA qmoA DVU0849 qmoB DVU1295 DVU1597 DVU2776 sat sir dsrC Purine biosynthesis DVU0161 DVU0488 DVU0795 purF purD purC Description Dissimilatory...”
- Temporal transcriptomic analysis as Desulfovibrio vulgaris Hildenborough transitions into stationary phase during electron donor depletion
Clark, Applied and environmental microbiology 2006 - “...primer (5-3) Size of amplicon (bp) DVU2776 DVU2571 DVU1311 DVU3108 DVU0014 DVU1858 DVU2839 DVU2061 AAGTCACTTACAAGGGCAAG CCAGCTTGAAGACATGGT TCACTGCCGAAGAGCTTA...”
- More
- Combining metabolic flux analysis with proteomics to shed light on the metabolic flexibility: the case of Desulfovibrio vulgaris Hildenborough.
Marbehan, Frontiers in microbiology 2024 - “...D DsvD Q46582 DVU_0404 8.8 7 60 3 Sulfite reductase, DsrABC complex, subunit C DsrC P45573 DVU_2776 11.9 14 66 7 Quinone oxidoreductase, QmoABC complex, subunit A QmoA Q72DT1 DVU_0848 44.6 82 78 28 Quinone oxidoreductase, QmoABC complex, subunit B QmoB Q72DT0 DVU_0849 82.5 211 85...”
- The life sulfuric: microbial ecology of sulfur cycling in marine sediments.
Wasmund, Environmental microbiology reports 2017 - “...Oliveira et al . ( 2008 ), and Venceslau et al . ( 2014 ) P45573 dsrMKJOP DsrMKJOP [DsrC]trisulfide hydrogen sulfide+[DsrC protein]dithiol+2 electrontransfer quinone Reduction of DsrC trisulfide, thereby linking cytoplasmic reduction of sulfite to energy conservation at membrane; reverse function in sulfur oxidation Grein et...”
SCL_1279 TusE/DsrC/DsvC family sulfur relay protein from Sulfuricaulis limicola
36% identity, 67% coverage
- The complete genome sequences of sulfur-oxidizing Gammaproteobacteria Sulfurifustis variabilis skN76(T) and Sulfuricaulis limicola HA5(T)
Umezawa, Standards in genomic sciences 2016 - “...and dsrC (SVA_0281, SVA_0284, SVA_0358, SVA_0917, SVA_0969, SVA_1205, SVA_1793, SVA_1949, SVA_2832, SVA_3655; SCL_0275, SCL_0524, SCL_0785, SCL_1279, SCL_1423, SCL_2646). As genes encoding proteins involved in oxidation of sulfite to sulfate in the cytoplasm, both genomes contain two copies of the aprAB genes encoding an adenosine-5-phosphosulphate reductase (SVA_2607-2608,...”
DMR_15890 sulfite reductase gamma subunit from Desulfovibrio magneticus RS-1
35% identity, 71% coverage
SVA_1793 TusE/DsrC/DsvC family sulfur relay protein from Sulfurifustis variabilis
34% identity, 62% coverage
- The complete genome sequences of sulfur-oxidizing Gammaproteobacteria Sulfurifustis variabilis skN76(T) and Sulfuricaulis limicola HA5(T)
Umezawa, Standards in genomic sciences 2016 - “...cluster, dsrAB (SVA_0258-0259, SCL_0256-0257), dsrS (SVA_2921, SCL_0781) and dsrC (SVA_0281, SVA_0284, SVA_0358, SVA_0917, SVA_0969, SVA_1205, SVA_1793, SVA_1949, SVA_2832, SVA_3655; SCL_0275, SCL_0524, SCL_0785, SCL_1279, SCL_1423, SCL_2646). As genes encoding proteins involved in oxidation of sulfite to sulfate in the cytoplasm, both genomes contain two copies of the...”
Dred_3197 DsrC family protein from Desulfotomaculum reducens MI-1
32% identity, 72% coverage
MHY1_00097 TusE/DsrC/DsvC family sulfur relay protein from Methylovirgula sp. HY1
36% identity, 58% coverage
- Sulfur and methane oxidation by a single microorganism
Gwak, Proceedings of the National Academy of Sciences of the United States of America 2022 - “..., 72 ). Notably, two additional DsrC-like proteins are encoded in strain HY1 (MHY1_00075 and MHY1_00097). Both lack Cys A and probably function as regulatory sulfur-related proteins (RpsA) ( 73 ). In strain HY1, sulfite formed by the rDsr pathway does not appear to be further...”
Dpo_5c02880 TusE/DsrC/DsvC family sulfur relay protein from Desulfotignum phosphitoxidans DSM 13687
31% identity, 72% coverage
Alvin_0028 sulfur relay protein, TusE/DsrC/DsvC family from Allochromatium vinosum DSM 180
33% identity, 33% coverage
- Evidence for autotrophic growth of purple sulfur bacteria using pyrite as electron and sulfur source
Alarcon, Applied and environmental microbiology 2024 - “...dsrC , there are four more genes annotated as TusE/DsrC/DsvC family sulfur relay proteins, namely Alvin_0028, Alvin_0345, Alvin_0732, and Alvin_1508 18 , which are, respectively, upregulated by ~2-, ~2-, and ~4-fold and downregulated by ~7-fold. In the sox loci, genes encoding SoxYZ complex were upregulated by...”
- “...dsrC , there are four more genes annotated as TusE/DsrC/DsvC family sulfur relay proteins, namely Alvin_0028, Alvin_0345, Alvin_0732, and Alvin_1508. We observed upregulation by ~2-fold to 4-fold for Alvin_0028, 0345, and 0732 and downregulation by ~8-fold for Alvin_1508. The dsr gene expression data are consistent with...”
- A comparative quantitative proteomic study identifies new proteins relevant for sulfur oxidation in the purple sulfur bacterium Allochromatium vinosum
Weissgerber, Applied and environmental microbiology 2014 - “...none of the conserved cysteine residues. Except for Alvin_0028, all DsrC homologs were detected in the proteome. The amount of Alvin_0345 decreased (Table 2),...”
- New proteins involved in sulfur trafficking in the cytoplasm of Allochromatium vinosum
Stockdreher, The Journal of biological chemistry 2014 - “...TusE (9). Neither CysA nor CysB is present in Alvin_0028 and Alvin_1508. These proteins are predicted to serve a regulatory function and have been termed...”
- Genome-wide transcriptional profiling of the purple sulfur bacterium Allochromatium vinosum DSM 180T during growth on different reduced sulfur compounds
Weissgerber, Journal of bacteriology 2013 - “...presence of sulfur compounds (Table 2). The genes Alvin_0028 and Alvin_0732 revealed less pronounced but still significantly increased relative mRNA levels on...”
- Complete genome sequence of Allochromatium vinosum DSM 180(T)
Weissgerber, Standards in genomic sciences 2011 - “...Besides dsrC, there are four more genes annotated as TusE/DsrC/DsvC family sulfur relay proteins, namely Alvin_0028, Alvin_0345, Alvin_0732 and Alvin_1508. Whether the encoded proteins are involved in dissimilatory sulfur metabolism and/ or thiouridine biosynthesis as reported for TusE in Escherichia coli [ 99 ] and possibly...”
Sfum_4045 DsrC family protein from Syntrophobacter fumaroxidans MPOB
29% identity, 72% coverage
- Complete genome sequence of Syntrophobacter fumaroxidans strain (MPOB(T))
Plugge, Standards in genomic sciences 2012 - “...predicted five-gene cluster along with genes that have high identity to dissimilatory sulfite reductase C (Sfum_4045). The gene organization of the alpha, beta and c-subunits of the whole cluster is different from other dissimilatory sulfate reducers [ 49 ]. Genes predicted to encode a membrane-bound dissimilatory...”
FTN_0548 hypothetical protein from Francisella tularensis subsp. novicida U112
41% identity, 62% coverage
- Molecular complexity orchestrates modulation of phagosome biogenesis and escape to the cytosol of macrophages by Francisella tularensis
Asare, Environmental microbiology 2010 - “...protein 3 tnfn1_pw060420p02q163 FTN_0398 hypothetical membrane protein 3 tnfn1_pw060420p04q104 FTN_0466 conserved hypothetical protein 4 tnfn1_pw060328p08q148 FTN_0548 conserved hypothetical protein 2 # tnfn1_pw060418p04q176 FTN_0548 conserved hypothetical protein 2 # tnfn1_pw060328p06q164 FTN_0630 hypothetical protein 5 tnfn1_pw060328p05q141 FTN_0701 conserved hypothetical protein 5 tnfn1_pw060418p02q152 FTN_0706 hypothetical membrane protein 3 tnfn1_pw060418p02q175...”
- Molecular bases of proliferation of Francisella tularensis in arthropod vectors
Asare, Environmental microbiology 2010 - “...protein 3 tnfn1_pw060420p02q163 FTN_0398 hypothetical membrane protein 3 tnfn1_pw060420p04q104 FTN_0466 conserved hypothetical protein 4 tnfn1_pw060328p08q148 FTN_0548 conserved hypothetical protein 2 # tnfn1_pw060418p04q176 FTN_0548 conserved hypothetical protein 2 # tnfn1_pw060328p06q164 FTN_0630 hypothetical protein 5 tnfn1_pw060328p05q141 FTN_0701 conserved hypothetical protein 5 tnfn1_pw060418p02q152 FTN_0706 hypothetical membrane protein 3 tnfn1_pw060418p02q175...”
SCL_2646 TusE/DsrC/DsvC family sulfur relay protein from Sulfuricaulis limicola
33% identity, 62% coverage
- The complete genome sequences of sulfur-oxidizing Gammaproteobacteria Sulfurifustis variabilis skN76(T) and Sulfuricaulis limicola HA5(T)
Umezawa, Standards in genomic sciences 2016 - “...(SVA_0281, SVA_0284, SVA_0358, SVA_0917, SVA_0969, SVA_1205, SVA_1793, SVA_1949, SVA_2832, SVA_3655; SCL_0275, SCL_0524, SCL_0785, SCL_1279, SCL_1423, SCL_2646). As genes encoding proteins involved in oxidation of sulfite to sulfate in the cytoplasm, both genomes contain two copies of the aprAB genes encoding an adenosine-5-phosphosulphate reductase (SVA_2607-2608, SVA_3565-3564; SCL_0600-0601,...”
KKC1_RS04165 TusE/DsrC/DsvC family sulfur relay protein from Calderihabitans maritimus
33% identity, 66% coverage
2xsjC / C7LV29 Structure of desulforubidin from desulfomicrobium norvegicum (see paper)
36% identity, 66% coverage
Alvin_1508 sulfur relay protein, TusE/DsrC/DsvC family from Allochromatium vinosum DSM 180
36% identity, 61% coverage
- Evidence for autotrophic growth of purple sulfur bacteria using pyrite as electron and sulfur source
Alarcon, Applied and environmental microbiology 2024 - “...1.9E-15 Dinitrogenase iron-molybdenum cofactor biosynthesis protein 117 Alvin_2429 2.95 8.1E-39 NADH-quinone oxidoreductase, B subunit 118 Alvin_1508 2.92 4.9E-23 Sulfur relay protein, TusE/DsrC/DsvC family 119 Alvin_1254 2.88 1.9E-19 DsrF 120 Alvin_2576 2.80 1.9E-02 Antenna complex alpha/beta subunit 121 Alvin_0501 2.79 2.6E-22 NusA antitermination factor 122 Alvin_2250 2.78...”
- “...four more genes annotated as TusE/DsrC/DsvC family sulfur relay proteins, namely Alvin_0028, Alvin_0345, Alvin_0732, and Alvin_1508 18 , which are, respectively, upregulated by ~2-, ~2-, and ~4-fold and downregulated by ~7-fold. In the sox loci, genes encoding SoxYZ complex were upregulated by 5-fold, whereas the rest...”
- A comparative quantitative proteomic study identifies new proteins relevant for sulfur oxidation in the purple sulfur bacterium Allochromatium vinosum
Weissgerber, Applied and environmental microbiology 2014 - “...Alvin_1365 Alvin_1366 Alvin_1394 Alvin_1502 Alvin_1503 Alvin_1508 Alvin_1848 Alvin_1971 Alvin_2001 Alvin_2107 Alvin_2019 Alvin_2037 Alvin_2038 Alvin_2136...”
- “...of Alvin_0345 decreased (Table 2), while that of Alvin_1508 increased significantly, on all sulfur compounds (Table 1). There is currently no experimental...”
- New proteins involved in sulfur trafficking in the cytoplasm of Allochromatium vinosum
Stockdreher, The Journal of biological chemistry 2014 - “...CysA nor CysB is present in Alvin_0028 and Alvin_1508. These proteins are predicted to serve a regulatory function and have been termed regulatory...”
- Genome-wide transcriptional profiling of the purple sulfur bacterium Allochromatium vinosum DSM 180T during growth on different reduced sulfur compounds
Weissgerber, Journal of bacteriology 2013 - “...Alvin_1394 Alvin_1395 Alvin_1398 Alvin_1420 Alvin_1468 Alvin_1508 Alvin_1713 Alvin_1737 Alvin_1740 Alvin_1741 Alvin_1848 Alvin_1918 Alvin_1920 Alvin_2001...”
- “...(25-fold increase in mRNA on elemental sulfur) and Alvin_1508 (6-fold increase on sulfide) showed highly elevated relative mRNA levels in the presence of sulfur...”
- Complete genome sequence of Allochromatium vinosum DSM 180(T)
Weissgerber, Standards in genomic sciences 2011 - “...four more genes annotated as TusE/DsrC/DsvC family sulfur relay proteins, namely Alvin_0028, Alvin_0345, Alvin_0732 and Alvin_1508. Whether the encoded proteins are involved in dissimilatory sulfur metabolism and/ or thiouridine biosynthesis as reported for TusE in Escherichia coli [ 99 ] and possibly in other cellular processes...”
Dde_0762 sulfite reductase, dissimilatory-type gamma subunit from Desulfovibrio desulfuricans G20
30% identity, 72% coverage
- Integration of text mining and biological network analysis: Identification of essential genes in sulfate-reducing bacteria
Saxena, Frontiers in microbiology 2023 - “...A aprA dde_1110 GO:0016491 Cysteine synthase A aprB dde_1109 GO:0046872; GO:0051536 Cysteine synthase A dsrC dde_0762 GO:0005737; GO:0018551 Sulfite reductase, dissimilatory-type gamma subunit CysH dde_1789 GO:0003824 Phosphoadenosine phosphosulfate reductase sat dde_2265 GO:0000103; GO:0004781; GO:0005524 Sulfate adenylyltransferase Transporters modB dde_3519 GO:0005886; GO:0015098; GO:0016021 Molybdate ABC transporter, inner...”
- “...Persistent (P) Shell (S) Cloud (C) Number of genes P S C Total Sulfur metabolism dde_0762, dde_1109, dde_1110, dde_0527, dde_0526, dde_2271, dde_3081, dde_1112, dde_2115, dde_2265, dde_3080, and dde_0528 dde_1789, sucD , dde_3604, and, dde_1258 dde_0123, dde_0276 12 4 2 18 Ribosome synthesis rpsM, rpsE, rpsD, fbp,...”
- Flexibility of syntrophic enzyme systems in Desulfovibrio species ensures their adaptation capability to environmental changes
Meyer, Journal of bacteriology 2013 - “...0.027 h 0.047 h 0.027 h 0.027 h1 in coculture Dde_0286 Dde_0762 / / / / / / / / / / a Gene annotation according to http//www.microbesonline.org (87), Pereira et...”
FOKN1_1941 TusE/DsrC/DsvC family sulfur relay protein from Thiohalobacter thiocyanaticus
31% identity, 68% coverage
LGS26_05895 TusE/DsrC/DsvC family sulfur relay protein from Dissulfurimicrobium hydrothermale
31% identity, 72% coverage
SCL_0785 TusE/DsrC/DsvC family sulfur relay protein from Sulfuricaulis limicola
46% identity, 43% coverage
- The complete genome sequences of sulfur-oxidizing Gammaproteobacteria Sulfurifustis variabilis skN76(T) and Sulfuricaulis limicola HA5(T)
Umezawa, Standards in genomic sciences 2016 - “...SCL_0781) and dsrC (SVA_0281, SVA_0284, SVA_0358, SVA_0917, SVA_0969, SVA_1205, SVA_1793, SVA_1949, SVA_2832, SVA_3655; SCL_0275, SCL_0524, SCL_0785, SCL_1279, SCL_1423, SCL_2646). As genes encoding proteins involved in oxidation of sulfite to sulfate in the cytoplasm, both genomes contain two copies of the aprAB genes encoding an adenosine-5-phosphosulphate reductase...”
LT988_03825 TusE/DsrC/DsvC family sulfur relay protein from Thiocapsa bogorovii
32% identity, 71% coverage
V8V93_13245 TusE/DsrC/DsvC family sulfur relay protein from Pseudodesulfovibrio methanolicus
31% identity, 66% coverage
SVA_0917 TusE/DsrC/DsvC family sulfur relay protein from Sulfurifustis variabilis
32% identity, 60% coverage
- The complete genome sequences of sulfur-oxidizing Gammaproteobacteria Sulfurifustis variabilis skN76(T) and Sulfuricaulis limicola HA5(T)
Umezawa, Standards in genomic sciences 2016 - “...of the gene cluster, dsrAB (SVA_0258-0259, SCL_0256-0257), dsrS (SVA_2921, SCL_0781) and dsrC (SVA_0281, SVA_0284, SVA_0358, SVA_0917, SVA_0969, SVA_1205, SVA_1793, SVA_1949, SVA_2832, SVA_3655; SCL_0275, SCL_0524, SCL_0785, SCL_1279, SCL_1423, SCL_2646). As genes encoding proteins involved in oxidation of sulfite to sulfate in the cytoplasm, both genomes contain two...”
Dpo_2c03440 TusE/DsrC/DsvC family sulfur relay protein from Desulfotignum phosphitoxidans DSM 13687
33% identity, 54% coverage
SVA_2832 TusE/DsrC/DsvC family sulfur relay protein from Sulfurifustis variabilis
33% identity, 62% coverage
- The complete genome sequences of sulfur-oxidizing Gammaproteobacteria Sulfurifustis variabilis skN76(T) and Sulfuricaulis limicola HA5(T)
Umezawa, Standards in genomic sciences 2016 - “...(SVA_0258-0259, SCL_0256-0257), dsrS (SVA_2921, SCL_0781) and dsrC (SVA_0281, SVA_0284, SVA_0358, SVA_0917, SVA_0969, SVA_1205, SVA_1793, SVA_1949, SVA_2832, SVA_3655; SCL_0275, SCL_0524, SCL_0785, SCL_1279, SCL_1423, SCL_2646). As genes encoding proteins involved in oxidation of sulfite to sulfate in the cytoplasm, both genomes contain two copies of the aprAB genes...”
SVA_0284 TusE/DsrC/DsvC family sulfur relay protein from Sulfurifustis variabilis
35% identity, 58% coverage
- The complete genome sequences of sulfur-oxidizing Gammaproteobacteria Sulfurifustis variabilis skN76(T) and Sulfuricaulis limicola HA5(T)
Umezawa, Standards in genomic sciences 2016 - “...genes outside of the gene cluster, dsrAB (SVA_0258-0259, SCL_0256-0257), dsrS (SVA_2921, SCL_0781) and dsrC (SVA_0281, SVA_0284, SVA_0358, SVA_0917, SVA_0969, SVA_1205, SVA_1793, SVA_1949, SVA_2832, SVA_3655; SCL_0275, SCL_0524, SCL_0785, SCL_1279, SCL_1423, SCL_2646). As genes encoding proteins involved in oxidation of sulfite to sulfate in the cytoplasm, both genomes...”
LT988_03875 TusE/DsrC/DsvC family sulfur relay protein from Thiocapsa bogorovii
31% identity, 59% coverage
SVA_0358 TusE/DsrC/DsvC family sulfur relay protein from Sulfurifustis variabilis
38% identity, 55% coverage
- The complete genome sequences of sulfur-oxidizing Gammaproteobacteria Sulfurifustis variabilis skN76(T) and Sulfuricaulis limicola HA5(T)
Umezawa, Standards in genomic sciences 2016 - “...outside of the gene cluster, dsrAB (SVA_0258-0259, SCL_0256-0257), dsrS (SVA_2921, SCL_0781) and dsrC (SVA_0281, SVA_0284, SVA_0358, SVA_0917, SVA_0969, SVA_1205, SVA_1793, SVA_1949, SVA_2832, SVA_3655; SCL_0275, SCL_0524, SCL_0785, SCL_1279, SCL_1423, SCL_2646). As genes encoding proteins involved in oxidation of sulfite to sulfate in the cytoplasm, both genomes contain...”
3or2C / E2QR99 Crystal structure of dissimilatory sulfite reductase ii (dsrii)
34% identity, 66% coverage
SCL_0524 TusE/DsrC/DsvC family sulfur relay protein from Sulfuricaulis limicola
33% identity, 62% coverage
- The complete genome sequences of sulfur-oxidizing Gammaproteobacteria Sulfurifustis variabilis skN76(T) and Sulfuricaulis limicola HA5(T)
Umezawa, Standards in genomic sciences 2016 - “...(SVA_2921, SCL_0781) and dsrC (SVA_0281, SVA_0284, SVA_0358, SVA_0917, SVA_0969, SVA_1205, SVA_1793, SVA_1949, SVA_2832, SVA_3655; SCL_0275, SCL_0524, SCL_0785, SCL_1279, SCL_1423, SCL_2646). As genes encoding proteins involved in oxidation of sulfite to sulfate in the cytoplasm, both genomes contain two copies of the aprAB genes encoding an adenosine-5-phosphosulphate...”
SCL_0275 TusE/DsrC/DsvC family sulfur relay protein from Sulfuricaulis limicola
34% identity, 55% coverage
- The complete genome sequences of sulfur-oxidizing Gammaproteobacteria Sulfurifustis variabilis skN76(T) and Sulfuricaulis limicola HA5(T)
Umezawa, Standards in genomic sciences 2016 - “...dsrS (SVA_2921, SCL_0781) and dsrC (SVA_0281, SVA_0284, SVA_0358, SVA_0917, SVA_0969, SVA_1205, SVA_1793, SVA_1949, SVA_2832, SVA_3655; SCL_0275, SCL_0524, SCL_0785, SCL_1279, SCL_1423, SCL_2646). As genes encoding proteins involved in oxidation of sulfite to sulfate in the cytoplasm, both genomes contain two copies of the aprAB genes encoding an...”
Alvin_0345 sulfur relay protein, TusE/DsrC/DsvC family from Allochromatium vinosum DSM 180
30% identity, 71% coverage
- Evidence for autotrophic growth of purple sulfur bacteria using pyrite as electron and sulfur source
Alarcon, Applied and environmental microbiology 2024 - “..., there are four more genes annotated as TusE/DsrC/DsvC family sulfur relay proteins, namely Alvin_0028, Alvin_0345, Alvin_0732, and Alvin_1508 18 , which are, respectively, upregulated by ~2-, ~2-, and ~4-fold and downregulated by ~7-fold. In the sox loci, genes encoding SoxYZ complex were upregulated by 5-fold,...”
- “..., there are four more genes annotated as TusE/DsrC/DsvC family sulfur relay proteins, namely Alvin_0028, Alvin_0345, Alvin_0732, and Alvin_1508. We observed upregulation by ~2-fold to 4-fold for Alvin_0028, 0345, and 0732 and downregulation by ~8-fold for Alvin_1508. The dsr gene expression data are consistent with the...”
- A comparative quantitative proteomic study identifies new proteins relevant for sulfur oxidation in the purple sulfur bacterium Allochromatium vinosum
Weissgerber, Applied and environmental microbiology 2014 - “...Annotation Sulfide Thiosulfate Sulfur Alvin_0082 Alvin_0345 Alvin_0809 Alvin_1102 Alvin_1420 Alvin_1848 Alvin_1890 Alvin_2032 Alvin_2033 Alvin_2093 Alvin_2247...”
- “...four more TusE/DsrC/DsvC family sulfur relay proteins (6): Alvin_0345 contains both, Alvin_0732 one, and the other DsrC homologs none of the conserved cysteine...”
- New proteins involved in sulfur trafficking in the cytoplasm of Allochromatium vinosum
Stockdreher, The Journal of biological chemistry 2014 - “...cysteine (CysB). One A. vinosum DsrC homolog (Alvin_0345) has both conserved cysteine residues. This protein has recently been proposed to functionally...”
- “...elemental sulfur and sulfite for Alvin_0732 and Alvin_0345. Construction of rhd_2599-, tusA-, and dsrE2-deficient A. vinosum Mutants--To further assess the...”
- Genome-wide transcriptional profiling of the purple sulfur bacterium Allochromatium vinosum DSM 180T during growth on different reduced sulfur compounds
Weissgerber, Journal of bacteriology 2013 - “...Alvin_0055 Alvin_0082 Alvin_0283 Alvin_0314 Alvin_0316 Alvin_0345 Alvin_0476 Alvin_0492 Alvin_0562 Alvin_0680 Alvin_0750 Alvin_0804 Alvin_0805 Alvin_0961...”
- “...family sulfur relay proteins (3). Among these, Alvin_0345 (25-fold increase in mRNA on elemental sulfur) and Alvin_1508 (6-fold increase on sulfide)...”
- Complete genome sequence of Allochromatium vinosum DSM 180(T)
Weissgerber, Standards in genomic sciences 2011 - “...dsrC, there are four more genes annotated as TusE/DsrC/DsvC family sulfur relay proteins, namely Alvin_0028, Alvin_0345, Alvin_0732 and Alvin_1508. Whether the encoded proteins are involved in dissimilatory sulfur metabolism and/ or thiouridine biosynthesis as reported for TusE in Escherichia coli [ 99 ] and possibly in...”
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory